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Commit aff3dce7 authored by Santiago Ospina De Los Ríos's avatar Santiago Ospina De Los Ríos
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Move logging configuration out of tests 

This helps to keep tests cleaner as well as centralizing logging settings.
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1 merge request!39Resolve "Improve testing on jacobians"
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test/test_jacobian.mini → test/logging.ini
+ 50
− 0
View file @ aff3dce7
_jacobian_type = numerical, analytical | expand
_name_sufix = {_jacobian_type}
__name = {_name_sufix}
[grid]
dimension = 2
file = grids/test_cell.msh
initial_level = 0
[model]
order = 1
jacobian_type = {_jacobian_type} # extra
[model.time_stepping]
rk_method = alexander_2
begin = 0.
end = 0.01
step = 2e-3
initial_step = 2e-3
min_step = 1e-3
max_step = 2e-3
decrease_factor = 0.9
increase_factor = 1.1
[model.writer]
file_path = {__name}
[model.compartments]
cell = 0
nucleoid = 1
############################ Model for cell ############################
[model.cell.initial]
u = 10
[model.cell.reaction]
u = -5*u
[model.cell.reaction.jacobian]
du_du = -5
[model.cell.diffusion]
u = 1.
############################ Model for nucleoid ############################
[model.nucleoid.initial]
u = 5
v = 10
[model.nucleoid.reaction]
u = -u*v
v = -10*u
[model.nucleoid.reaction.jacobian]
du_du = -v
du_dv = -u
dv_du = -10
dv_dv = 0
[model.nucleoid.diffusion]
u = 1.
v = 1.
######################### Compare with reference vtk #########################
[wrapper.vtkcompare]
name = {__name}/{__name}-cell-00005 {__name}/{__name}-nucleoid-00005
reference = reference/cell-00005 reference/nucleoid-00005
extension = vtu vtu
relative = 2e-2
absolute = 1e-9
############################ Logging settings #################################
# levels = off, critical, error, waring, notice, info, detail, debug, trace, all
......@@ -91,7 +20,7 @@ level = off
# General info go into this logger
# Settings on this logger are the default values for other backend loggers
[logging.default]
level = detail
level = trace
indent = 0
sinks = logfile, stdout
......@@ -102,17 +31,17 @@ indent = 0
# Grid info go into this logger
[logging.backend.grid]
level = detail
level = trace
indent = 2
# General model info go into this logger
[logging.backend.model]
level = detail
level = trace
indent = 2
# Time stepping info go into this logger
[logging.backend.stepper]
level = detail
level = trace
indent = 4
# writer info go into this logger
......
test/NFKappaB.mini → test/test_NFkappaB.mini
+ 7
− 53
View file @ aff3dce7
__name = NFkappaB
# Test: Check that complicated problems have an approximately same analytic and
# numeric jacobian
import logging.ini
__name = test_NFkappaB
[grid]
dimension = 2
......@@ -12,7 +17,7 @@ order = 1
rk_method = alexander_2
begin = 0.
end = 365
step = 1e-3
initial_step = 1e-0
min_step = 1e-3
max_step = 1e-0
decrease_factor = 0.9
......@@ -248,54 +253,3 @@ IkBa_nucleus = 1
p65_IkB_nucleus = 1
IkBa_mRNA_nucleus = 1
IkBa_mRNA_1 = 1
############################ Logging settings #################################
# levels = off, critical, error, waring, notice, info, detail, debug, trace, all
# Sink setup for console stdcout
[logging.sinks.stdout]
level = info # max level to output on this sink
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Sink setup for logfile output
[logging.sinks.logfile]
level = all # max level to output on this sink
type = rank-0-file
file = {__name}.log
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Logger internal info go into this logger
[logging.internal]
level = off
# General info go into this logger
# Settings on this logger are the default values for other backend loggers
[logging.default]
level = detail
indent = 0
sinks = logfile, stdout
# Logger info go into this logger
[logging.backend.logging]
level = off
indent = 0
# Grid info go into this logger
[logging.backend.grid]
level = detail
indent = 2
# General model info go into this logger
[logging.backend.model]
level = detail
indent = 2
# Time stepping info go into this logger
[logging.backend.stepper]
level = detail
indent = 4
# writer info go into this logger
[logging.backend.writer]
level = trace
indent = 4
test/test_cell.mini
+ 5
− 51
View file @ aff3dce7
# Test: Compare a simple multidomain diffusion-reaction problem with respect
# to a reference solution produced by stable versions of the program
import logging.ini
__name = test_cell
[grid]
......@@ -65,54 +70,3 @@ reference = reference/cell-00005 reference/nucleoid-00005
extension = vtu vtu
relative = 2e-2
absolute = 1e-9
############################ Logging settings #################################
# levels = off, critical, error, waring, notice, info, detail, debug, trace, all
# Sink setup for console stdcout
[logging.sinks.stdout]
level = info # max level to output on this sink
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Sink setup for logfile output
[logging.sinks.logfile]
level = all # max level to output on this sink
type = rank-0-file
file = {__name}.log
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Logger internal info go into this logger
[logging.internal]
level = off
# General info go into this logger
# Settings on this logger are the default values for other backend loggers
[logging.default]
level = detail
indent = 0
sinks = logfile, stdout
# Logger info go into this logger
[logging.backend.logging]
level = off
indent = 0
# Grid info go into this logger
[logging.backend.grid]
level = detail
indent = 2
# General model info go into this logger
[logging.backend.model]
level = detail
indent = 2
# Time stepping info go into this logger
[logging.backend.stepper]
level = detail
indent = 4
# writer info go into this logger
[logging.backend.writer]
level = trace
indent = 4
test/test_exp.mini
+ 2
− 51
View file @ aff3dce7
import logging.ini
_grow_rate = 0.2
_initial = 1
_geometry_type = cubes, triangles | expand geometry_type
......@@ -45,54 +47,3 @@ u = 0.
u = exp({_grow_rate}*t)
[model.domain.compare.l2_error]
u = 2.4e-4
############################ Logging settings #################################
# levels = off, critical, error, waring, notice, info, detail, debug, trace, all
# Sink setup for console stdcout
[logging.sinks.stdout]
level = info # max level to output on this sink
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Sink setup for logfile output
[logging.sinks.logfile]
level = all # max level to output on this sink
type = rank-0-file
file = {__name}.log
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Logger internal info go into this logger
[logging.internal]
level = off
# General info go into this logger
# Settings on this logger are the default values for other backend loggers
[logging.default]
level = detail
indent = 0
sinks = logfile, stdout
# Logger info go into this logger
[logging.backend.logging]
level = off
indent = 0
# Grid info go into this logger
[logging.backend.grid]
level = detail
indent = 2
# General model info go into this logger
[logging.backend.model]
level = detail
indent = 2
# Time stepping info go into this logger
[logging.backend.stepper]
level = detail
indent = 4
# writer info go into this logger
[logging.backend.writer]
level = trace
indent = 4
test/test_gauss.mini
+ 5
− 51
View file @ aff3dce7
# Test: Check that the first steps of a pure diffusive problem evolve as a
# gaussian process
import logging.ini
_diffusion = 0.005
_t0 = 1.
_gauss_eq = exp(-((x-0.5)^2+(y-0.5)^2)/(4*t*{_diffusion})) / (4*pi*t*{_diffusion})
......@@ -47,54 +52,3 @@ u = {_diffusion}
u = {_gauss_eq}
[model.domain.compare.l2_error]
u = 0.255 , 0.076 | expand geometry_type
############################ Logging settings #################################
# levels = off, critical, error, waring, notice, info, detail, debug, trace, all
# Sink setup for console stdcout
[logging.sinks.stdout]
level = info # max level to output on this sink
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Sink setup for logfile output
[logging.sinks.logfile]
level = all # max level to output on this sink
type = rank-0-file
file = {__name}.log
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Logger internal info go into this logger
[logging.internal]
level = off
# General info go into this logger
# Settings on this logger are the default values for other backend loggers
[logging.default]
level = detail
indent = 0
sinks = logfile, stdout
# Logger info go into this logger
[logging.backend.logging]
level = off
indent = 0
# Grid info go into this logger
[logging.backend.grid]
level = detail
indent = 2
# General model info go into this logger
[logging.backend.model]
level = detail
indent = 2
# Time stepping info go into this logger
[logging.backend.stepper]
level = detail
indent = 4
# writer info go into this logger
[logging.backend.writer]
level = trace
indent = 4
test/test_gauss_mixed_geometry.mini
+ 3
− 51
View file @ aff3dce7
# Test: Check that the first steps of a pure diffusive problem evolve as a
# gaussian process (mixed geometry version)
__name = test_gauss_mixed_geometry
_diffusion = 0.005
......@@ -66,54 +69,3 @@ u = {_diffusion}
u = {_gauss_eq}
[model.triangles.compare.l2_error]
u = 0.095
############################ Logging settings #################################
# levels = off, critical, error, waring, notice, info, detail, debug, trace, all
# Sink setup for console stdcout
[logging.sinks.stdout]
level = info # max level to output on this sink
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Sink setup for logfile output
[logging.sinks.logfile]
level = all # max level to output on this sink
type = rank-0-file
file = {__name}.log
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Logger internal info go into this logger
[logging.internal]
level = off
# General info go into this logger
# Settings on this logger are the default values for other backend loggers
[logging.default]
level = detail
indent = 0
sinks = logfile, stdout
# Logger info go into this logger
[logging.backend.logging]
level = off
indent = 0
# Grid info go into this logger
[logging.backend.grid]
level = detail
indent = 2
# General model info go into this logger
[logging.backend.model]
level = detail
indent = 2
# Time stepping info go into this logger
[logging.backend.stepper]
level = detail
indent = 4
# writer info go into this logger
[logging.backend.writer]
level = trace
indent = 4
test/test_in_out.mini
+ 3
− 52
View file @ aff3dce7
# Test that checks fluxes on membranes with a reference vtk file produced with
# previous versions of dune_copasi_md
import logging.ini
__name = test_in_out
[grid]
......@@ -75,55 +78,3 @@ p65_nucleus = 0.01
[model.writer]
file_path = {__name}
############################ Logging settings #################################
# levels = off, critical, error, waring, notice, info, detail, debug, trace, all
# Sink setup for console stdcout
[logging.sinks.stdout]
level = info # max level to output on this sink
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Sink setup for logfile output
[logging.sinks.logfile]
level = all # max level to output on this sink
type = rank-0-file
file = {__name}.log
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Logger internal info go into this logger
[logging.internal]
level = off
# General info go into this logger
# Settings on this logger are the default values for other backend loggers
[logging.default]
level = detail
indent = 0
sinks = logfile, stdout
# Logger info go into this logger
[logging.backend.logging]
level = off
indent = 0
# Grid info go into this logger
[logging.backend.grid]
level = detail
indent = 2
# General model info go into this logger
[logging.backend.model]
level = detail
indent = 2
# Time stepping info go into this logger
[logging.backend.stepper]
level = detail
indent = 4
# writer info go into this logger
[logging.backend.writer]
level = trace
indent = 4
test/test_initial.mini
+ 5
− 52
View file @ aff3dce7
# Test: Check the interpolation output for math expression initialization
import logging.ini
_diffusion = 0.01
_t0 = 1.
_gauss_eq = exp(-((x-0.5)^2+(y-0.5)^2)/(2.*t*{_diffusion})) / (2*pi*t*{_diffusion})
_gauss_eq = exp(-((x-0.5)^2+(y-0.5)^2)/(4*t*{_diffusion})) / (4*pi*t*{_diffusion})
_geometry_type = cubes, triangles | expand geometry_type
__name = test_initial_{_geometry_type}
......@@ -48,54 +52,3 @@ u = {_diffusion}
u = {_gauss_eq}
[model.domain.compare.l2_error]
u = 7e-2, 5e-3 | expand geometry_type
############################ Logging settings #################################
# levels = off, critical, error, waring, notice, info, detail, debug, trace, all
# Sink setup for console stdcout
[logging.sinks.stdout]
level = info # max level to output on this sink
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Sink setup for logfile output
[logging.sinks.logfile]
level = all # max level to output on this sink
type = rank-0-file
file = {__name}.log
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Logger internal info go into this logger
[logging.internal]
level = off
# General info go into this logger
# Settings on this logger are the default values for other backend loggers
[logging.default]
level = detail
indent = 0
sinks = logfile, stdout
# Logger info go into this logger
[logging.backend.logging]
level = off
indent = 0
# Grid info go into this logger
[logging.backend.grid]
level = detail
indent = 2
# General model info go into this logger
[logging.backend.model]
level = detail
indent = 2
# Time stepping info go into this logger
[logging.backend.stepper]
level = detail
indent = 4
# writer info go into this logger
[logging.backend.writer]
level = trace
indent = 4
test/test_no_writer.mini
+ 4
− 53
View file @ aff3dce7
# Test: An inifile without `writer` section must be valid
import logging.ini
__name = test_no_writer
[grid]
......@@ -33,56 +37,3 @@ du_du = 1
[model.domain.diffusion]
u = 0.
# A inifile without `writer` section must be valid
############################ Logging settings #################################
# levels = off, critical, error, waring, notice, info, detail, debug, trace, all
# Sink setup for console stdcout
[logging.sinks.stdout]
level = info # max level to output on this sink
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Sink setup for logfile output
[logging.sinks.logfile]
level = all # max level to output on this sink
type = rank-0-file
file = {__name}.log
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Logger internal info go into this logger
[logging.internal]
level = off
# General info go into this logger
# Settings on this logger are the default values for other backend loggers
[logging.default]
level = detail
indent = 0
sinks = logfile, stdout
# Logger info go into this logger
[logging.backend.logging]
level = off
indent = 0
# Grid info go into this logger
[logging.backend.grid]
level = detail
indent = 2
# General model info go into this logger
[logging.backend.model]
level = detail
indent = 2
# Time stepping info go into this logger
[logging.backend.stepper]
level = detail
indent = 4
# writer info go into this logger
[logging.backend.writer]
level = trace
indent = 4
test/test_tiff.mini
+ 4
− 52
View file @ aff3dce7
# Test that checks interpolation of TIFF files with a reference vtk file
# Test: Checks interpolation of TIFF files with a reference vtk file
# produced with previous versions of dune_copasi_sd/md
import logging.ini
__name = test_tiff
[grid]
......@@ -50,54 +53,3 @@ reference = reference/{__name}-00000
extension = vtu
relative = 2e-2
absolute = 1e-9
############################ Logging settings #################################
# levels = off, critical, error, waring, notice, info, detail, debug, trace, all
# Sink setup for console stdcout
[logging.sinks.stdout]
level = info # max level to output on this sink
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Sink setup for logfile output
[logging.sinks.logfile]
level = all # max level to output on this sink
type = rank-0-file
file = {__name}.log
pattern = "[\\{reldays:0>2\\}-\\{reltime:8%T\\}] [\\{backend\\}] \\{msg\\}"
# Logger internal info go into this logger
[logging.internal]
level = off
# General info go into this logger
# Settings on this logger are the default values for other backend loggers
[logging.default]
level = detail
indent = 0
sinks = logfile, stdout
# Logger info go into this logger
[logging.backend.logging]
level = off
indent = 0
# Grid info go into this logger
[logging.backend.grid]
level = detail
indent = 2
# General model info go into this logger
[logging.backend.model]
level = detail
indent = 2
# Time stepping info go into this logger
[logging.backend.stepper]
level = detail
indent = 4
# writer info go into this logger
[logging.backend.writer]
level = trace
indent = 4
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